[BioC] too many biomaRt connections

[Sean Davis]

On Wed, Apr 9, 2008 at 3:32 PM, Steffen <sdurinck at lbl.gov> wrote:
> Hi Elizabeth,
>
>  This is an error I've recently encountered as well and has as far as I
>  know nothing to do with the number of queries you performed but is a
>  more general problem of the BioMart version of Ensembl.
>  biomaRt is not the only tool querying this web service.  Other tools
>  like Taverna and custom tools using e.g. the BioMart perl API also query
>  this web service.
>  It looks like the BioMart system has gained popularity and recently we
>  frequently hit the maximum number of connections to the MySQL database.
>  Note that biomaRt doesn't query directly via MySQL but it's the MySQL
>  connection at the web service that is unable to connect.
>
>  I've contacted the Ensembl and BioMart teams and they are investigating
>  this problem.  It would help reporting this to helpdesk at ensembl.org to
>  pressure them on this issue, showing it's not only me but many people
>  who can't use their web service recently.  Report this part of the error
>  message:
>
>
>  Too many connections at
>  /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm
>  line 98
>
>
>  Cheers,
>  Steffen

Just to finish the thought here, it is possible to install the MySQL
database locally and use biomaRt locally.  I think this will solve the
problem for those who need regular, uninterrupted access.  Steffen can
correct me if I'm wrong on this.  Also, installing is not for the
faint-of-heart, as the database is pretty big.

Sean


>
>
>  Elizabeth Purdom wrote:
>  > Hi,
>  > I am using biomaRt to get information regarding genes. I use it pretty
>  > frequently and recently have gotten the error:
>  >
>  > Too many connections at
>  > /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm
>  > line 98
>  >
>  > I assume that I've hit some sort of wall in terms of how often I have
>  > queried the database?
>  >
>  > I don't really use biomart except through R; at what point do you get
>  > booted off and what can I do to regain access? I often run queries on a
>  > few hundred genes and don't think twice about rerunning such a query or
>  > running several such queries in a day plus I use functions that call on
>  > biomaRt repeatedly that I also apply to around 100 genes. So I could
>  > easily send a thousand queries in a day. I can be more careful, but it
>  > would be useful to know what the limits are. And does it matter how many
>  > times you call a 'mart<-useMart(...)' command? (lately, I've been
>  > calling it frequently rather than using the one I've already opened,
>  > largely through programming laziness).
>  >
>  > By the way, it took me quite some time to track down the error, because
>  > I was using getGene which just gave me the confusing error:
>  > "Error: ncol(result) == length(attributes) is not TRUE"
>  > I think this must be because something like try(...) is used within
>  > getBM() and so the output is the error message which is then transferred
>  > down the line and at some point causes a problem when the function tries
>  > to bundle it into a data.frame, etc.
>  >
>  > Thanks,
>  > Elizabeth
>  >
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>
>  --
>  ----------------------------------------------------------------
>  Steffen Durinck, PhD
>
>  Division of Biostatistics, University of California, Berkeley &
>  Life Sciences Department, Lawrence Berkeley National Laboratory
>  1 cyclotron Rd, Berkeley
>  CA, 94720, USA
>  Tel: +1-510-486-5202
>
>
>
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